{
    "title": "Invocation manifest for BIDS Freesurfer: Freesurfer recon-all BIDS App",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "properties": {
        "config": {
            "type": "object",
            "properties": {
                "participant_label": {
                    "type": "string"
                },
                "session_label": {
                    "type": "string"
                },
                "n_cpus": {
                    "type": "integer"
                },
                "stages": {
                    "default": "autorecon-all",
                    "type": "string"
                },
                "steps": {
                    "type": "string"
                },
                "template_name": {
                    "default": "average",
                    "type": "string"
                },
                "acquisition_label": {
                    "type": "string"
                },
                "refine_pial_acquisition_label": {
                    "type": "string"
                },
                "multiple_sessions": {
                    "default": "longitudinal",
                    "enum": [
                        "longitudinal",
                        "multiday"
                    ],
                    "type": "string"
                },
                "refine_pial": {
                    "default": "T2",
                    "enum": [
                        "T2",
                        "FLAIR",
                        "None",
                        "T1only"
                    ],
                    "type": "string"
                },
                "hires_mode": {
                    "default": "auto",
                    "enum": [
                        "auto",
                        "enable",
                        "disable"
                    ],
                    "type": "string"
                },
                "parcellations": {
                    "default": "aparc",
                    "type": "string"
                },
                "measurements": {
                    "default": "thickness",
                    "type": "string"
                },
                "skip_bids_validator": {
                    "default": false,
                    "type": "boolean"
                },
                "3T": {
                    "type": "boolean"
                },
                "gear-analysis-level": {
                    "default": "participant",
                    "type": "string",
                    "enum": [
                        "participant",
                        "group1",
                        "group2"
                    ]
                },
                "gear-abort-on-bids-error": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-log-level": {
                    "default": "INFO",
                    "type": "string",
                    "enum": [
                        "ERROR",
                        "WARNING",
                        "INFO",
                        "DEBUG"
                    ]
                },
                "gear-run-bids-validation": {
                    "default": true,
                    "type": "boolean"
                },
                "gear-dry-run": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-keep-output": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-FREESURFER_LICENSE": {
                    "type": "string"
                }
            },
            "required": [
                "stages",
                "template_name",
                "multiple_sessions",
                "refine_pial",
                "hires_mode",
                "parcellations",
                "measurements",
                "skip_bids_validator",
                "gear-analysis-level",
                "gear-abort-on-bids-error",
                "gear-log-level",
                "gear-run-bids-validation",
                "gear-dry-run",
                "gear-keep-output"
            ]
        },
        "inputs": {
            "type": "object",
            "properties": {
                "key": {
                    "type": "object"
                },
                "freesurfer_license": {
                    "type": "object",
                    "properties": {}
                },
                "bids_validator_config": {
                    "type": "object",
                    "properties": {}
                }
            },
            "required": [
                "key"
            ]
        }
    },
    "required": [
        "config",
        "inputs"
    ]
}